Detection of mitochondrial single nucleotide polymorphisms using a primer elongation reaction on oligonucleotide microarrays

Nucleic Acids Research

Volumn 29, Issue 7, 2020, Pages

  Erdogan, Fikret ^a,b   Kirchner, Roland ^a   Mann, Wolfgang ^a   Ropers, Hans Hilger ^a   Nuber, Ulrike A ^a  

^a MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

^b FREIE UNIVERSITÄT BERLIN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

DNA POLYMERASE; EXONUCLEASE; GENOMIC DNA; GLASS; MITOCHONDRIAL DNA; OLIGONUCLEOTIDE; PHOSPHOROTHIOIC ACID; PRIMER DNA; SINGLE STRANDED DNA;

ARTICLE; CONTROLLED STUDY; COVALENT BOND; DNA SEQUENCE; HUMAN; MICROARRAY ANALYSIS; MITOCHONDRION; OLIGONUCLEOTIDE MICROARRAY; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; ALLELE; BASE MISPAIRING; DNA MICROARRAY; GENETICS; METHODOLOGY;

ALLELES; BASE PAIR MISMATCH; DNA PRIMERS; DNA, MITOCHONDRIAL; DNA, SINGLE-STRANDED; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OLIGONUCLEOTIDES; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE NUCLEOTIDE;

MLCS; MLOWN;

EID: 0035315802     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/29.7.e36     Document Type: Article

References (30)

1. Brookes, A.J. (1999) The essence of SNPs. Gene, 234, 177-186.
2. Zhao, L.P., Aragaki, C., Hsu, L. and Quiaoit, F. (1998) Mapping of complex traits by single-nucleotide polymorphisms. Am. J. Hum.Genet., 63, 225-240.
3. Cargill, M., Altshuler, D., Ireland, J., Sklar, P., Ardlie, K., Patil, N., Lane, C.R., Lim, E.P., Kalyanaraman, N., Nemesh, J. et al. (1999) Characterization of single-nucleotide polymorphisms in coding regions of human genes. Nat. Genet., 22, 231-238.
4. Halushka, M.K., Fan, J.B., Bentley, K., Hsie, L., Shen, N., Weder, A., Cooper, R., Lipshutz, R. and Chakravarti, A. (1999) Patterns of single-nucleotide polymorphisms in candidate genes for blood-pressure homeostasis. Nat. Genet., 22, 239-247.
5. Kruglyak, L. (1999) Prospects for whole-genome linkage disequilibrium mapping of common disease genes. Nat. Genet., 22, 139-144.
6. Mc Carthy, J.J. and Hilfiker, R. (2000) The use of single-nucleotide polymorphism maps in pharmacogenomics. Nat. Biotechnol., 18, 505-508.
7. Housman, D. and Ledley, F.D. (1998) Why pharmacogenomics? Why now? Nat. Biotechnol., 16 (Suppl.), 2-3.
8. Nielsen, R. (2000) Estimation of population parameters and recombination rates from single nucleotide polymorphisms. Genetics, 154, 931-942.
9. Hacia, J.G., Fan, J.B., Ryder, O., Jin, L., Edgemon, K., Ghandour, G., Mayer, R.A., Sun, B., Hsie, L., Robbins, C.M. et al. (1999) Determination of ancestral alleles for human single-nucleotide polymorphisms using high-density oligonucleotide arrays., Nat. Genet., 22, 164-167.
10. Kruglyak, L. (1997) The use of a genetic map of biallelic markers in linkage studies. Nat. Genet., 17, 21-24.
11. Guo, Z., Guilfoyle, R.A., Thiel, A.J., Wang, R. and Smith, L.M. (1994) Direct fluorescence analysis of genetic polymorphisms by hybridization with oligonucleotide arrays on glass supports. Nucleic Acids Res., 22, 5456-5465.
12. Hacia, J.G., Brody, L.C., Chee, M., S., Fodor, S.P.A. and Collins, F.S. (1996) Detection of heterozygous mutations in BRCA1 using high density oligonucleotide arrays and two-colour fluorescence analysis. Nat. Genet., 14, 441-447.
13. Hacia, J.G. (1999) Resequencing and mutational analysis using oligonucleotide microarrays. Nat. Genet., 21, 42-47.
14. Winzeler, E.A., Richards, D.R., Conway, A.R., Goldstein, A.L., Kalman, S., Mc Cullough, M.J., Mc Cusker, J.H., Stevens, D.A., Wodicka, L., Lockhart, D.J. et al. (1998) Direct allelic variation scanning of the yeast genome. Science, 281, 1194-1197.
15. Wang, D.G., Fan, J.B., Siao, C.J., Berno, A., Young, P., Sapolsky, R., Ghandour, G., Perkins, N., Winchester, E., Spencer, J. et al. (1998) Large-scale identification, mapping and genotyping of single-nucleotide polymorphisms in the human genome. Science, 280, 1077-1082.
16. Conner, B.J., Reyes, A.A., Morin, C., Itakura, K., Teplitz, R.L. and Wallace, R.B. (1983) Detection of sickle cell β S-globin allele by hybridization with synthetic oligonucleotides. Proc. Natl Acad. Sci. USA, 80, 278-282
17. Southern, E.M., Maskos, U. and Elder, J.K. (1992) Analyzing and comparing nucleic acid sequences by hybridization to arrays of oligonucleotides: evaluation using experimental models. Genomics, 13, 1008-1017.
18. Sosnowski, R.G., Tu, E., Butler, W.F., O'Connel, J.P. and Heller, M.J. (1997) Rapid determination of single base mismatch mutations in DNA hybrids by direct electric field control. Proc. Natl Acad. Sci. USA, 94, 1119-1123.
19. Gilles, P.N., Wu, D.J., Foster, C.B., Dillon, P.J. and Chanock, S.J. (1999) Single nucleotide polymorphic discrimination by an electronic dot blot assay on semiconductor microchips. Nat. Biotechnol., 17, 365-370.
20. Nguyen, H.K., Fournier, O., Asseline, U., Dupret, D. and Nguyen, T.T. (1999) Smoothing of the thermal stability of DNA duplexes by using modified nucleosides and chaotropic agents. Nucleic Acids Res., 27, 1492-1498.
21. Gunderson, K.L., Huang, X.C., Morris, M.S., Lipshutz, R.J., Lockhart, D.J. and Chee, M.S. (1998) Mutation detection by ligation to complete n-mer DNA arrays. Genome Res., 8, 1142-1153.
22. Pastinen, T., Kurg, A., Metspalu, A., Peltonen, L. and Syvänen, A.C. (1997) Minisequencing: a specific tool for DNA analysis and diagnostics on oligonucleotide arrays. Genome Res., 7, 606-614.
23. Pastinen, T., Raitio, M., Lindroos, K., Tainola, P., Peltonen, L. and Syvänen, A.C. (2000) A system for specific, high-throughput genotyping by allele-specific primer extension on microarrays. Genome Res., 10, 1031-1042.
24. Dubiley, S., Kirillov, E. and Mirzabekov, A. (1999) Polymorphism analysis and gene detection by minisequencing on an array of gel-immobilized primers. Nucleic Acids Res., 27, e19.
25. Hofmann, S., Jaksch, M., Bezold, R., Mertens, S., Aholt, S., Paprotta, A. and Gerbitz, K.D. (1997) Population genetics and disease susceptibility: characterization of central European haplogroups by mtDNA gene mutations, correlation with D loop variants and association with disease. Hum. Mol. Genet., 6, 1835-1846.
26. Wallace, D.C. (1999) Mitochondrial diseases in man and mouse. Science, 283, 1482-1488.
27. Liang, M.H. and Wong, L.J. (1998) Yield of mtDNA mutation analysis in 2, 000 patients. Am. J. Med. Genet., 77, 395-400.
28. Butler, J.M. and Levin, B.C. (1998) Forensic applications of mitochondrial DNA. Trends Biotechnol., 16, 158-162.
29. Huang, M.M., Arnheim, N. and Goodman, M.F. (1992) Extension of base mispairs by Taq DNA polymerase: implications for single nucleotide discrimination in PCR. Nucleic Acids Res., 20, 4567-4573.
30. Nikiforov, T.T., Rendle, R.B., Goelet, P., Rogers, Y.H., Kotewicz, M.L., Anderson, S., Trainor, G.L. and Knapp, M.R. (1994) Genetic Bit Analysis: a solid phasemethod for typing single nucleotide polymorphisms. Nucleic Acids Res., 22, 4167-4175.